cycledash

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For example, letting the developer know if the test server cannot be started

jaclynperrone

Support both HDFS and NFS/other file systems for BAM files

6

for uploaded BAM files

jaclynperrone

Allow 3+ BAMs to be visualized in pileup.js on Examine page

3

ihodes

API.md and about.html; one should be generated from the other, most likely.

ihodes

Deprecate links to IGV

1

We should use this issue to catalogue IGV features missing from pileup.js

hammer

IGV integration doesn't work with VCFs on NFS

2

The "Load at Locus" link sends IGV to `http://hammerlab-dev3.hpc.mssm.edu:9876file:///tmp/one-samplexxx.vcf`, which doesn't work.

danvk

Link between CycleDash and UCSC Genome Browser

4

ihodes

It looks like we intend to, but the error message "BAM not found." doesn't appear in the response body, like it should.

ihodes

Cf. #800; may be possible now with https://bvaughn.github.io/react-virtualized/?

hammer

PyVCF failing to parse Strelka VCF

2

cf. http://cycledash.demeter.hpc.mssm.edu/tasks/249 ``` Traceback (most recent call last): File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task R = retval = fun(*args, **kwargs) File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py", line 437, in __protected_call__ return self.run(*args, **kwargs) File...

ihodes